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Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain.

ABSTRACT: Chromosome substitution strains (CSS or consomic strains) are useful for mapping phenotypes to chromosomes. However, huge efforts are needed to identify the gene(s) responsible for the phenotype in the complex context of the chromosome. Here we report the identification of candidate disease genes from a CSS by using a combination of genetic and genomic approaches and by using knowledge about the germ cell tumor disease etiology. We used the CSS 129.MOLF-Chr19 chromosome substitution strain, in which males develop germ cell tumors of the testes at an extremely high rate. We were able to identify three protein-coding genes and one microRNA on chromosome 19 that have previously not been implicated to be testicular tumor susceptibility genes. Our findings suggest that changes in gene expression levels in the gonadal tissues of multiple genes from Chr 19 likely contribute to the high testicular germ cell tumor (TGCT) incidence of the 129.MOLF-Chr19 strain. Our data advance the use of CSS to identify disease susceptibility genes and demonstrate that the 129.MOLF-Chr19 strain serves as a useful model to elucidate the genetics and biology of germ cell transformation and tumor development.

SUBMITTER: Zhu R

PROVIDER: S-EPMC2647748 | biostudies-literature | 2007 Aug

REPOSITORIES: biostudies-literature

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Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain.

Zhu Rui R Ji Yuan Y Xiao Lianchun L Matin Angabin A

Mammalian genome : official journal of the International Mammalian Genome Society 20070802 8

Chromosome substitution strains (CSS or consomic strains) are useful for mapping phenotypes to chromosomes. However, huge efforts are needed to identify the gene(s) responsible for the phenotype in the complex context of the chromosome. Here we report the identification of candidate disease genes from a CSS by using a combination of genetic and genomic approaches and by using knowledge about the germ cell tumor disease etiology. We used the CSS 129.MOLF-Chr19 chromosome substitution strain, in w ...[more]

PMID: 17671812

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Project description:Chromosome substitution strains (CSS or consomic strains) are useful for mapping phenotypes to chromosomes. However, huge efforts are needed to identify the gene(s) responsible for the phenotype in the complex context of the chromosome. Here, we report the identification of candidate disease genes from a CSS using a combination of genetic and genomic approaches as well as by using knowledge about the germ cell tumor disease etiology. We utilized the CSS, 129.MOLF-Chr 19 chromosome substitution strain (or M19), in which males develop germ cell tumors of the testes at an extremely high rate. We are able to identify 3 protein-coding genes and 1 microRNA on chromosome 19 that have previously not been implicated to be testicular tumor susceptibility genes. Our findings suggest that changes in gene expression levels in the gonadal tissues of multiple genes from Chr 19 likely contribute to the high TGCT incidence of the M19 strain. Our data advances the use of CSS to identify disease susceptibility genes and demonstrates that the 129.MOLF-Chr 19 strain serves as a useful model to elucidate the genetics and biology of germ cell transformation and tumor development. For gene expression profiling, we used male gonads from different developmental stages, E13.5 and PN1, from the M19 and 129 strains. The idea was to detect the common gene expression changes in the gonads at stages when germ cells are known to transform to embryonal carcinoma (EC) cells. E13.5 stage was chosen because tumor development is reported to start around E13.5 in 129 strains (Stevens 1973b; Stevens and Hummel 1957). PN1 stage gonads were chosen because our studies with M19;Oct4-GFP mice, as described above, showed that both germ cells and EC cells are present at this stage suggesting that germ cell transformation may also be ongoing at this stage in the testes of M19 strain. We also compared gene expression differences in gonads to that of embryos to determine whether gene expression differences are specific to the gonads. Our goal was to identify gene(s) whose expression is consistently changed in the gonads at E13.5 and PN1 in the M19 as these would likely be candidate TGCT susceptibility gene(s). Fig. 3A indicates the 3 different tissue samples collected from the M19 and 129 strains: gonads (genital ridges) dissected from male E13.5 embryos and from PN1 mice and male embryos at E13. Because tumor incidence in M19 is approximately 80% we anticipated that gene expression changes could be masked because ~20% of cells/tissues within a sample may have normal levels of gene expression or 20% of the testes may have normal gene expression. Moreover, the amount of RNA extracted from a single genital ridge or PN1 testis is insufficient for a microarray experiment. To minimize the effect of individual samples and to isolate sufficient RNA for microarray analysis from these small sized gonads, we pooled RNA from multiple samples (Table 1). Six RNA pooled samples were prepared (Fig.3A and Supplementary Table 2): E13.5 gonad RNA from males of 129 (129-GR) and M19 (M1-GR); PN1 testes RNA from 129 (129-NBT) and M19 (M1-NBT); E13.5 embryo RNA from males of 129 (129-E) and M19 (M1-E). The six RNA samples were hybridized to six Affymetrix mouse genome genechips individually. Hierarchical clustering analysis revealed a dendrogram in which gene expression profiles of the same tissue type clustered together (Fig. 3B). Profiles of the gonads, E13.5 and PN1, were related more closely than to those of embryos. Comparison of the expression profiles of E13.5 gonads from M19 and 129 revealed 10 genes with more than a 2-fold difference in expression levels (Fig. 3A and Supplementary Table 3A). Six of the 10 genes mapped to Chr 19. For the PN1 testes, 266 genes showed significant fold changes between the two strains and of these 13 genes mapped to Chr 19 (Fig. 3A and Supplementary Table 3C). For the E13.5 embryos, 35 genes showed greater than a 2-fold change in expression between the M19 and 129 and 5 out of 35 genes mapped to Chr 19 (Fig. 3A and Supplementary Table 3B). By analyzing the data of differentially expressed genes present in the 3 samples, as well as selecting those that map to Chr 19, we were able to exclude a majority of the genes but found 3 genes in common. The 3 genes map to Chr 19 and were found to be downregulated in the M19 strain E13.5 and PN1 gonads as well as E13.5 embryos. These are Zfp162, D19Bwg1357e and Cox15. These 3 genes have not been previously implicated in testicular tumorigenesis and are novel TGCT candidate susceptibility genes.

Project description:Cancer-testis (CT) genes are a group of genes restrictedly expressed in testis and multiple cancers and can serve as candidate driver genes participating in the development of cancers. Our previous study identified a number of CT genes in nongerm cell tumors, but their expression pattern in testicular germ cell tumor (TGCT), a cancer type characterized by less genomic alterations, remained largely unknown. In this study, we systematically investigated the expression pattern of CT genes in TGCT samples and evaluated the transcriptome difference between TGCT and normal testis tissues, using datasets from the UCSC Xena platform, The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Pathway enrichment analysis and survival analysis were conducted to evaluate the biological function and prognostic effect of expressed CT genes. We identified that 1036 testis-specific expressed protein-coding genes and 863 testis-specific expressed long noncoding RNAs (lncRNAs) were expressed in TGCT samples, including 883 CT protein-coding genes and 710 CT lncRNAs defined previously. The number of expressed CT genes was significantly higher in seminomas (P = 3.48 × 10-13 ) which were characterized by frequent mutations in driver genes (KIT, KRAS and NRAS). In contrast, the number of expressed CT genes showed a moderate negative correlation with the fraction of copy number altered genomes (cor = -0.28, P = 1.20 × 10-3 ). Unlike other cancers, our analysis revealed that 96.16% of the CT genes were down-regulated in TGCT samples, while CT genes in stem cell maintenance related pathways were up-regulated. Further survival analysis provided evidence that CT genes could also predict the prognosis of TGCT patients with both disease-free interval and progression-free interval as clinical endpoints. Taken together, our study provided a global view of CT genes in TGCT and provided evidence that CT genes played important roles in the progression and maintenance of TGCT.

Dataset Information

Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain.

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Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain.

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